LBN_bin_plot: Biomass size spectrum plot for binned data demonstrating...

In andrew-edwards/sizeSpectra: Fitting Size Spectra to Ecological Data Using Maximum Likelihood

Biomass size spectrum plot for binned data demonstrating uncertainties

Usage

LBN_bin_plot(
  binValsTibble = NULL,
  binBreaks = NULL,
  binCounts = NULL,
  b.MLE,
  b.confMin,
  b.confMax,
  plot.binned.fitted = TRUE,
  log.xy = "xy",
  xLim = NA,
  yLim = NA,
  rect.col = "grey",
  logLabels = FALSE,
  xLabel.small = c(2, 5, 20, 50, 200, 500),
  yLabel.small = c(5, 50, 500),
  xLab = expression(paste("Body mass ", italic(x), "(g)")),
  yLab = "Normalised biomass",
  x.PLB = NA,
  legend = TRUE,
  leg.pos = "topright",
  inset = c(0, 0),
  leg.text = "(a)",
  ...
)

Arguments

binValsTibble	tibble of binned data with each row representing a bin and with columns binMin and binMmax (min and max break of each bin) and binCount (count in that bin), as in the binVals component of the output of binData. wmin and wmax can also be used instead of binMin and binMax. Extra columns are ignored.
binBreaks	vector of bin breaks
binCounts	vector of bin counts
b.MLE	maximum likelihood estimate of b (ideally from the MLEbin method)
b.confMin	lower 95\ \item b.confMaxupper 95\ \item plot.binned.fittedif TRUE then also plot the estimated normalised biomass in each bin for the MLE of b and it's confidence limits \item log.xyWhich axes to log, for plot(..., log = log.xy). So "xy" for log-log axes, "x" for only x-axis logged, "" for both axes unlogged. \item x.PLBvector of values to use to plot the fitted PLB curve; if NA then automatically calculated \item legendif TRUE then add legend \item leg.posposition of legend, from "bottomright"', '"bottom"', '"bottomleft"', '"left"', '"topleft"', '"top"', '"topright"', '"right"' and '"center"'. \item insetinset distance vector for legend \item leg.texttext for legend \item ...further arguments to be passed to plot() and plot_binned_fitted() TODO should return a tibble of results Biomass size spectrum plot for binned data, showing the bin widths explicitly and the normalised biomass in each bin (with resulting uncertainties). So extending MEE Fig. 6 for already binned data, using a new approach motivated by MEPS Fig. 7. Should probably then be recommended to replace MEE Fig. 6. Axes are logged, and labelled as either logged or (more intuitive) logged values. See vignette MLEbin_recommend.Rmd. Bin breaks and counts are input as EITHER a single tibble binValsTibble with each row representing a bin, OR as vectors binBreaks and binCounts. Andrew Edwards

andrew-edwards/sizeSpectra documentation built on June 28, 2023, 7:09 p.m.